MmuINT0028649 @ mm10
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:6013589-6014065:-
Coord C1 exon
chr19:6013996-6014065
Coord A exon
chr19:6013708-6013995
Coord C2 exon
chr19:6013589-6013707
Length
288 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGC
5' ss Score
6.03
3' ss Seq
GAGGGTCTTTCCTATTCCAGGGG
3' ss Score
8.31
Exon sequences
Seq C1 exon
GAACTGATGTCAAACCCCCAGTTCATCGTGGATGGAGCCACCCGGACAGACATCTGCCAGGGAGCACTGG
Seq A exon
GTAGGCCCCCAGGGGTGGGGTTCTGGGCGTTTGCCCCATTGTAGTTCTCCGTTCCCGTTCCATTGGGCACTGCCCCAACTCCTCCCTCCTGCAGGTCCAGACAGGTTTTGACTATCAGCATAGGTGCTGGTTCGCCCAGATTCCTGGGTCTTTTCTGTAAGCGGAGGGGAGATGAAGGGTACCCCACCCAGGGAATCCCTGGTGGCCCCCGGCATCCCACATACACAGCACCTCCCTCCCCTGGGCAGATCCGGAAAGCAAGCCTGATGAGGGTCTTTCCTATTCCAG
Seq C2 exon
GGGACTGTTGGCTCCTGGCTGCCATTGCCTCCCTCACCCTCAACGAGACTATTCTGCACCGAGTGGTTCCCTACGGCCAGAGCTTTCAGGATGGCTACGCTGGCATCTTTCATTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942:ENSMUST00000025891:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(37.1=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(13.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACTGATGTCAAACCCCCAGT
R:
TGGAAATGAAAGATGCCAGCGT
Band lengths:
188-476
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types